A self assembled molecular zipper based on a perfluorophenyl-phenyl diacetylene motif

Article abstract of DOI:10.1039/b517759f

The synthesis and characterization of a molecular rod consisting of a pentafluorophenyl and a para-dodecylphenyl subunit linked by a diacetylene and its large area self assembly into perfect parallel lines consisting of interlocked molecular rods are reported and discussed. The Royal Society of Chemistry 2006.

Full text of DOI:10.1039/b517759f

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COMMUNICATION
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A self assembled molecular zipper based on a perfluorophenyl-phenyl
diacetylene motif
Lijin Shu,a Zhongcheng Mu,b Harald Fuchs,b Lifeng Chi*b and Marcel Mayor*ac
Received (in Cambridge, UK) 15th December 2005, Accepted 20th February 2006
First published as an Advance Article on the web 20th March 2006
DOI: 10.1039/b517759f
1
characterized by H-NMR and 13C-NMR spectroscopy, electron
The synthesis and characterization of a molecular rod consist-
impact mass spectroscopy and elemental analysis.
ing of a pentafluorophenyl and a para-dodecylphenyl subunit
linked by a diacetylene and its large area self assembly into
perfect parallel lines consisting of interlocked molecular rods
are reported and discussed.
To investigate the self assembly properties of 1 on HOPG, a
droplet of solution 1 (concentration near saturation) in phenyl-
octane was applied to a freshly cleaved HOPG surface. Subsequent
investigation of the surface by STM displayed perfectly ordered
parallel stripes consisting of alternating bright and dark regions
covering the whole observed surface. To demonstrate the extent
of the surface structuring effect, Fig. 1 displays a typical 210 6
210 nm large area completely covered with the stripe pattern.
Perfluorophenyl and phenyl substituted diacetylenes attracted our
attention as the first reported example of a supramolecular stacked
diacetylene was said to result in a cis-polybutadiyne upon
photopolymerization in the solid state.1 The p–p stacking
interaction between benzene and hexafluorobenzene has already
been reported in 1960 by Patrick and Prosser.2 The supramolecular
synthon has meanwhile been investigated in detail and has been
applied successfully in crystal engineering,3 topochemistry4 and
even to preorganize reactants.5 Furthermore, the synthon allowed
the tuning of the material properties of liquid crystals,6 polymers,6
hydrogels7 and even biomolecules like DNA duplexes.8 To
investigate the properties of the supramolecular synthon on the
surface, we further functionalized a 1-pentafluorophenyl-4-phenyl-
butadiyne rod with a dodecyl alkyl chain to increase solubility,
processability and also surface packing properties.
˚
The dimensions of the observed stripes are a width of about 19 A
˚
for the brighter ribbons and 12 A for the darker lines clearly in the
range of the size of the molecules. The first hypothesis was the
formation of stripes due to the aryl-perfluoroaryl stacking synthon.
However, higher resolution of the STM pictures enabled a closer
inspection of the self assembly properties of 1 on the graphite
surface. As displayed in Fig. 2, the bright ribbons consist of
dumbbell shaped bright spots with the size of the rigid molecular
rod substructure of 1. These dumbbell structures consist of a
brighter outside unit and a less intense inside unit. These inside
units interlock like a zipper and combine two rows of dumbbell
structures to form the bright ribbons. The periodicity of the
structure has been measured along the white line in Fig. 2.
Calibration with the underlaying graphite gave a periodic distance
Here we report the synthesis and the self assembly properties on
a graphite (HOPG) surface of the molecular rod 1, consisting of a
diacetylene linked pentafluorophenyl and para-dodecylphenyl
subunit.
˚
between two bright spots of 10.6 A. The spacing is much too large
As displayed in Scheme 1, the synthesis of 1 is based on a
Cadiot–Chodkiewicz9 coupling between the bromoacetylene 4 and
the acetylene 8.{ Starting from commercial pentafluorobenzalde-
hyde 2, a Corey–Fuchs10 reaction sequence gave the bromoace-
tylene 4 in good yield. To assemble 8, 1,4-dibromobenzene 5 was
first functionalized with a dodecyl chain in a Grignard reaction to
afford 6. A subsequent Sonogashira reaction11 gave the trimethyl-
silyl (TMS)-protected acetylene 7, which was deprotected to afford
8 in good yield. A Pd/Cu catalyzed variation12 of the Cadiot–
Chodkiewicz coupling in N-ethyldiisopropylamine at room
temperature gave the desired rod 1 in 35% yield, after column
chromatography, as a white solid.{ All compounds have been
to explain the self assembly pattern with an aryl-perfluoroaryl
stacking synthon, which displays a spacing in the solid state of
1
about 3.7 A. The relatively large spacing between two dumbbell
˚
structures rather points at a flat arrangement of the rigid rod on
the graphite substrate. As fluor-atoms are known to appear less
visible in an STM experiment,13 the less intense center parts of the
self assembled ribbons consist of the pentafluoroaryl subunits.
aForschungszentrum Karlsruhe GmbH, Institute for Nanotechnology,
Postfach 3640, 76021 Karlsruhe, Germany.
E-mail: marcel.mayor@int.fzk.de; Fax: +49 7247 82 5685;
Tel: +49 7247 82 6392
bWestfaelische Wilhelm-Universitaet Muenster, Physikalisches Institut,
Wilhelm-Klemm-Str. 10, 48149 Muenster, Germany.
E-mail: chi@uni-muenster.de; Fax: +49 251 8333602;
Tel: +49 251 8333651
cUniversita¨t Basel, Departement Chemie, St. Johannsring 19, 4056 Basel,
Switzerland. E-mail: marcel.mayor@unibas.ch; Fax: +41 61 267 1016;
Tel: +41 61 267 1006
Scheme 1 Synthesis of the molecular rod 1.
1862 | Chem. Commun., 2006, 1862–1863
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In conclusion we have synthesized a pentafluorophenyl and
phenyl substituted diacetylene with an additional dodecyl chain to
investigate self assembly properties on surfaces. Upon wet
deposition on HOPG, huge areas of perfectly ordered patterns
of parallel bright stripes are observed. A closer inspection of the
structure unravels a zipper like interlocked pattern of the molecular
rod as the origin of the bright stripes. The intercalating dodecyl
chain results in the separate dark regions between the bright
stripes. Packing parameters leading to the surface patterns are
supported by intermolecular interactions, in particular of the
pentafluorophenyl and diacetylene subunits and of the alkyl
chains.
The authors acknowledge the support with a postdoctoral
position for L. S. by the Center for Functional Nanostructures
(CFN) of the Deutsche Forschungsgemeinschaft (DFG) within
project C3.
Notes and references
Fig. 1 Pattern of parallel stripes on an HOPG surface covered with 1.
{ Bromoacetylene 4 (0.7 g; 2.6 mmol), acetylene 8 (0.7 g; 2.6 mmol),
Pd2(dba)3CHCl3 (0.08 g; 0.08 mmol; 3 mol%), CuI (0.02 g; 0.1 mmol;
4 mol%) and N-ethyldiisopropylamine (0.5 ml) in toluene (25 ml) was
degassed with nitrogen and stirred at room temperature for 10 hours. After
evaporation of the solvent, column chromatography on SiO2 with hexane
as the eluent gave 1-pentafluorophenyl-4-(49-dodecylphenyl)butadiyne 1
(0.42 g; 0.91 mmol; 35%) as a white solid. Mp: 38 uC. 1H NMR (CDCl3)
dH: 0.94 (t, 3H), 1.31 (br, 18H), 1.35 (m, 2H), 1.66 (q, 2H), 2.67 (t, 2H), 7.20
(d, 2H), 7.49 (d, 2H). 13C NMR (CDCl3) dC: 14.00, 22.72, 29.31, 29.40,
29.50, 29.62, 29.69 (br), 29.72, 31.08, 31.98, 36.10, 64.27 (q, J = 4.0 Hz),
72.30, 85.63, 85.82 (q, J = 3.2 Hz), 99.60 (td, J = 17.8 Hz, J = 4.0 Hz),
117.88, 128.67, 132.67, 137.75 (dm (doublet of multiplet), J = 255 Hz),
142.00 (dm, J = 255 Hz), 145.69, 148.30 (dm, J = 255 Hz). EI-MS m/z
460.3 [M+]. Anal. calcd for C28H29F5: C, 73.03; H, 6.35. Found: C, 73.14;
H, 6.07%.
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Fig. 2 STM image of the self assembled ribbons consisting of 1. A model
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A model of the molecular rod 1 has been overlayed onto the
STM image (Fig. 2). The excellent fit between the STM picture
and the molecular model further confirms and illustrates the self
assembled molecule as the origin of the surface pattern. Obviously
the dark regions separating two parallel bright ribbons by about
˚
12 A are due to the intercalating dodecyl chains. However, the
STM picture does not allow individual dodecyl chains to be
resolved and hence, two arrangements differing in the direction of
the kink between the rod and the dodecyl chain are possible. The
perfectly parallel aligned dodecyl chains favour the packing
displayed in Fig. 2. To our surprise, neither the aryl-perfluoroaryl
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3e,14
…
stacking synthon nor C–H F hydrogen bonds
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are dominat-
ing the self assembly of 1 on the HOPG surface. The dense
arrangement of the pentafluoroaryl subunits in the centre of
…
the bright ribbon rather support F F interactions together with
…
C–F
p
interactions as potential intermolecular forces.
Furthermore the packing suggests a stabilizing interaction between
the electronegative fluorine atoms and the electron rich diethynyl
linkers.
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